PORT ANGELES — Cooke Aquaculture has agreed to pay $2.75 million to settle with the Wild Fish Conservancy over alleged Clean Water Act violations related to the collapse of Cooke’s Cypress Island net pen.

Those funds will go to the Rose Foundation to fund environmental projects to protect wild salmon and killer whales in Puget Sound, as well as WFC’s litigation expenses, according to a press release. Cooke also agreed to change its practices and address additional concerns identified in the lawsuit.

“This is truly a victory for the future of our sound,” said Kurt Beardslee, executive director of Wild Fish Conservancy. “Open water net pen aquaculture is a risky business, and thanks to this settlement we are one step closer to getting this dirty industry out of Puget Sound once and for all.”

Earlier this year Cooke Aquaculture, which owns a fish farm off Ediz Hook, agreed to pay a $332,000 fine for releasing 250,000 non-native fish that breached its compromised Cypress Island facility in August 2017.

Wild Fish Conservancy issued a notice of violations in August 2017, days after the Cypress Island pen collapsed and spilled Atlantic salmon infected with an exotic virus into Puget Sound.

Cooke announced in October that it was teaming up with the Jamestown S’Klallam Tribe to restart its dormant fish farm in the Port Angeles Harbor. Public comment on that project closed Nov. 22.

Trial in the federal lawsuit was set to begin Dec. 2. Days before the trial, U.S. District Judge John Coughenour issued several summary judgments supporting WFC’s claims.

The court found that Cooke failed to conduct required inspections of net pen moorings and anchors and that Cooke failed to accurately monitor and report the number of fish escaping form its pens.

Cooke had argued that it should not have to pay civil penalties because its pen was destroyed and no longer operates, an assertion Coughenour rejected.

“Now, it seems clear that Cypress 2 is permanently closed, but Defendant continues its operations in Puget Sound,” Coughenour wrote. “Thus, civil penalties still serve to deter future Clean Water Act violations.”

“We’re thankful for the Judge’s ruling and hope the severity of these penalties will be a deterrent to anyone seeking to expand or establish open water net pen aquaculture in Puget Sound and beyond,” Beardslee said.

The agreement with Cooke requires Cooke to conduct load analysis before restocking its facilities.

It must also complete any “upgrades, modifications and/or replacements determined to be necessary to meet applicable safety standards.”

Cooke is required to notify the WFC within two weeks of completion of upgrades, modifications or replacements.

The company will also create records for each inspection of the mooring system or main cage system and maintain those records for at least three years.

Of the $2.75 million settlement, $1.15 million will go to the Rose Foundation for Communities and the Environment, which will be paid no later than June 30, 2022.

The remaining $1.6 million covers litigation expenses and costs, including attorney and expert fees.

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Reporter Jesse Major can be reached at 360-452-2345, ext. 56250, or at jmajor@peninsula dailynews.com.